1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145
|
af385205c47f62b62c572b00020c82bd *DESCRIPTION
285016804af5c87628377926ac8b21a9 *NAMESPACE
a4fff23b4696800df6623db4395f5d14 *NEWS
4b3df28877eabd59c0a65a9a428ee242 *R/AllClasses.R
e001e076ad2cfa7932bd24bd11db98b2 *R/AllGenerics.R
0dd0e8605c4582835e15d09168e2d2aa *R/AllUtilities.R
697a1867aab01194bce703429a3ea656 *R/makeVRangesFromGRanges.R
686c78875cb73313205ca0836140c424 *R/methods-CollapsedVCF-class.R
72ff9653f3cb9db1206e79bef500aa3e *R/methods-ExpandedVCF-class.R
f6d29208384e706bf5379e39b505dcf7 *R/methods-PROVEANDb.class.R
16e0cda42e2b9689fda91a5e0241162b *R/methods-PolyPhenDb-class.R
d00445aab0435f46e054203d3d0c36a9 *R/methods-SIFTDb-class.R
c5dc0b9a30bc04a228ff764222ce3e1e *R/methods-ScanVcfParam-class.R
7b529c1454a59fa98f15ddac0078da68 *R/methods-VCF-class.R
fa49a082aacad1750f172c8f42a26a3d *R/methods-VCFHeader-class.R
b4b5b5eac87f3114e23deac77639eeb4 *R/methods-VRanges-class.R
a0c9f023af6acb24a78c02be2ed8d3e1 *R/methods-VRangesList-class.R
b1a88d4287ee9fd6ba4a1ed34cb710b6 *R/methods-VariantType-class.R
bce35ce459c8f6957059b7780217a40f *R/methods-VcfFile.R
727fd9d194dc00bd3ce9658e7896b97d *R/methods-expand.R
838f570879f793899e92abd36353c813 *R/methods-filterVcf.R
1ede20b5f7b930250ceba5559027f06a *R/methods-genotypeToSnpMatrix.R
12e427935431a8497731df7ac6f5ebba *R/methods-import.R
f253a6e26971ab940fdca51fd923cca9 *R/methods-locateVariants.R
b6c58f8cb8dfac1f46500091265621b0 *R/methods-predictCoding.R
eca153a42808ec03ba3757df7026b2c9 *R/methods-readVcf.R
d1fffcd2337227aff0eadbd23b76b3f5 *R/methods-scanVcf.R
cd79449e4e2b1340c42adda8518be8e1 *R/methods-scanVcfHeader.R
8750a8f0b2fd3e63ba74b11bec0c5e92 *R/methods-snpSummary.R
03ade37c141018adea71016066976bc8 *R/methods-summarizeVariants.R
628c838d57109692e52ab0b22409b4d9 *R/methods-writeVcf.R
4e1a2554e0f160df47326d99f536d1ca *R/test_VariantAnnotation_package.R
89a8c69cc4e2ed99b2a7489cbe9e24c6 *R/use_vep_api.R
bab7d0095c84012a05c20dd0fd79abcb *build/vignette.rds
d78e5d4bfb7b395cc500293e255d3365 *inst/CITATION
40df59dddb59fb1c2e34c0e04f830769 *inst/doc/VariantAnnotation.R
f0718d7188ef8d41ef2896978b203e5b *inst/doc/VariantAnnotation.Rmd
6a77cea5caabed8ef811dfd86030b2bc *inst/doc/VariantAnnotation.html
06f80ba0d7620a0e6b4c643d41fde84f *inst/doc/ensemblVEP.R
c0424a9efefad07f22be4677ee2c2037 *inst/doc/ensemblVEP.Rmd
4a72f7956f94d1e4c0afb955a40b3ec6 *inst/doc/ensemblVEP.html
99ee5f62dc678d273976634521db055a *inst/doc/filterVcf.R
9437f0796f440360ce0daffdb87e7cb1 *inst/doc/filterVcf.Rmd
2c18d326a39e9521b491db843d9b8feb *inst/doc/filterVcf.html
46e78a67f51161387c4c13aeefe80367 *inst/extdata/chr22.vcf.gz
540ee7e114a2c3c9f9730610940ec47f *inst/extdata/chr22.vcf.gz.tbi
a4ca21413e322997ed17c5429e65b9ca *inst/extdata/chr7-sub.vcf.gz
dc5c0ecc784ff39509a164f3020b72f8 *inst/extdata/chr7-sub.vcf.gz.tbi
b325a60a320b6aebb41d41d1dafb9c6d *inst/extdata/ex2.vcf
277341ce20f406ab09a0c23c6bd0d86f *inst/extdata/gl_chr1.vcf
f2a805083bd71e155f977ffb49df2cd5 *inst/extdata/h1187-10k.vcf.gz
fab30e49f0d054d462f8e1737844b204 *inst/extdata/h1187-10k.vcf.gz.tbi
f2a16449fa12afad25f21aceb90c1f9d *inst/extdata/hapmap_exome_chr22.vcf.gz
4bc7a2ff10bc925d4d5801c32c644ade *inst/extdata/hapmap_exome_chr22.vcf.gz.tbi
48852d332eb21dd639b4c6be53762357 *inst/extdata/structural.vcf
17f1c6f05e7a9ff7756b6efabce3f745 *inst/scripts/test_Rplinkseq.R
b7a9592a5de31dd84a3f7e8d1e0332de *inst/unitTests/cases/FORMAT_header_no_SAMPLEs.vcf
9ce56b3cbbb6829d3e3236a106046da0 *inst/unitTests/cases/VarScan_header.vcf
0c5f14796bf4eb3683ceff8e559f43d7 *inst/unitTests/cases/banded_gvcf.vcf
0fbb3e914d7a97208d8d1eb8fcb93026 *inst/unitTests/cases/buffer_realloc.vcf
992d76f76b4634d6ea263b873f92cbac *inst/unitTests/cases/ex1-seq1-90.vcf
4619ce5ed3abf69b38c13f8a72ca9755 *inst/unitTests/cases/expand.vcf
7be3dfdcd77d28fe84fdeb30ea096d58 *inst/unitTests/cases/fewer-FORMAT-than-GENO.vcf
dfc226165c7c64d2e24a1fe952600cdd *inst/unitTests/cases/meta_header.vcf
3d07a0b85a80b389b0ee5ba3dba11b13 *inst/unitTests/cases/missing-FORMAT-metadata-elt.vcf
ba4c3b28d5f63740fda11e70a19eccd7 *inst/unitTests/cases/mixedStructural.vcf
0230db3391a4a664fd5e2236fd0e5a92 *inst/unitTests/cases/multiple_INFO_fields.vcf
752d9d47c17d8f66791ce8804d88dbf6 *inst/unitTests/cases/negative_FORMAT_Number.vcf
39d8ae8aa155e4bac07e9215017143e7 *inst/unitTests/cases/no_FORMAT_column.vcf
4fc8b2f12f8b054e888ce092bb5b5443 *inst/unitTests/cases/no_GENO_row.vcf
a99d3b281abdd928c30fd147de3848a0 *inst/unitTests/cases/no_INFO_header.vcf
0c5bd63cfafbad13a8591b4963e0d411 *inst/unitTests/cases/unspecified_INFO_FORMAT_fields.vcf
0b5b4448b336d5a5b56d18cf818f9712 *inst/unitTests/test_SIFTandPolyPhen.R
d08510e74b080b9d0830a1941740ea90 *inst/unitTests/test_ScanVcfParam-class.R
dedcdc316629cb8661cc893f6d18da0f *inst/unitTests/test_VCF-class.R
cfafe68af5016d10de6557a41a9ec030 *inst/unitTests/test_VRanges-class.R
98f30f7a93c9bb3ea1605f693d02b569 *inst/unitTests/test_expand-methods.R
ad687c9f6717a20333e98db69fe89286 *inst/unitTests/test_filterVcf.R
7c00151d0528b740a94ddb9a8504898a *inst/unitTests/test_genotypeToSnpMatrix.R
2c2205ed5a0c6d352887365ce90f025a *inst/unitTests/test_isSNV.R
5c303ea47fa41a2fcc89f6c834c5d83e *inst/unitTests/test_locateVariants-methods.R
b92e0e7b951b75b850b37d0204efa1f5 *inst/unitTests/test_predictCoding-methods.R
5044be812d16c430cbc3a2451c10eba4 *inst/unitTests/test_readVcf-methods.R
16a5eae70d0e330c6660e94f57fdf32f *inst/unitTests/test_scanVcf.R
e45debe5cc9e5a797032c5ece476a74c *inst/unitTests/test_snpSummary.R
d98bfd1bf44ccafabe740b9ae42d1208 *inst/unitTests/test_summarizeVariants-methods.R
118c0fdfd316bc754c56babc45b3bbdf *inst/unitTests/test_vcfFields.R
d3bb2d2fe3e1d082db457d14f0c9d7e6 *inst/unitTests/test_writeVcf-methods.R
1bca1c23f953949c8ea4032f84453f58 *man/GLtoGP.Rd
1a62acad369f75e5acaac5d2710484c1 *man/PROVEANDb-class.Rd
4424810d10ddaa68f3c2c79e523613dc *man/PolyPhenDb-class.Rd
5768a4e9ac668eb3d4e20989d0c8895c *man/PolyPhenDbColumns.Rd
fe86efd2d798051da079492a2136ccfc *man/SIFTDb-class.Rd
ef5ca2ca2c777a11b47d0fdecde8f81d *man/SIFTDbColumns.Rd
3130885b3f5986a6ad775a0814dbd0e9 *man/ScanVcfParam-class.Rd
0194f7e5660ff8dbeaa396634cf85fce *man/VCF-class.Rd
358c3edbeec290bebbaa34997b76bf18 *man/VCFHeader-class.Rd
c52c9eeff59f08a10670c2074245a418 *man/VRanges-class.Rd
3773d0bb16b29dc2a37a5dbce4fb854d *man/VRangesList-class.Rd
0c3c4b5aef77601ede50c171ebdab4cd *man/VariantType-class.Rd
7b3d7ad20e8736bb5b97179276b6cf43 *man/VcfFile-class.Rd
eaee7546e931f4dea490e04a32cbc079 *man/defunct.Rd
3935884a8df80fcd28fda709e34493fd *man/filterVcf-methods.Rd
8774e086855172e4fbf918ae5719e646 *man/genotypeToSnpMatrix-methods.Rd
a19d100fb317e61e39222ec045c1a443 *man/getTranscriptSeqs-methods.Rd
30e36860989a8e8cb98190d825ebd8fa *man/indexVcf-method.Rd
081c7005fcde09f60ba1d99eb1789966 *man/isSNV-methods.Rd
902beb119a6acde24f427b83eca6c28c *man/locateVariants-methods.Rd
76ab75fa60be36da9546c88638efafd6 *man/post_Hs_region.Rd
648486d29f189d186f36128884582276 *man/predictCoding-methods.Rd
5da8862ce9f7d6cff350c398a6697aa0 *man/probabilityToSnpMatrix.Rd
bb0c9a4c80112203967409929138acc1 *man/readVcf-methods.Rd
990567974560df0115b60f9def9f0e26 *man/scanVcf-methods.Rd
56162c4890ba425b0b29457c1fb8f0fb *man/seqinfo-method.Rd
5c2b4326e0628a4b6193f6ecdbfdf451 *man/snpSummary.Rd
d5b2f73f157ffe7ece128b6c4b6cb6d7 *man/summarizeVariants-methods.Rd
e7b877b8dc3a6c4f7226ee3e2d983199 *man/variant_body.Rd
6de8ca2d4d6c75f25e86affcb11b699c *man/vep_by_region.Rd
b74173cf3462507a557463ce9860e50b *man/writeVcf-methods.Rd
f1f4685a8f0afb74e19c344a86d86b22 *src/Biostrings_stubs.c
b0447144238dce005a1fa8a625d1563c *src/IRanges_stubs.c
7b8d1c2c8939e293615971dd97729f83 *src/Makevars
75d2b4b077d8b1693d03fa896ccf7bd5 *src/R_init_VariantAnnotation.c
07fbf9ef7d1a296302e6de26aa821a44 *src/XVector_stubs.c
e838f1083f5fdaf8a707fe3da4e75f46 *src/dna_hash.c
4618f802de2f8627ac69bc22d284dab2 *src/dna_hash.h
8515d6330f973f17a522d2a00261ecbf *src/rle.c
8079f1a2260ac100fb302a58e61687ef *src/rle.h
96766323a50ab9af5616658cf9f4131d *src/strhash.c
ac7ab13dc6a3d23b75deaec4407cf566 *src/strhash.h
3aa83f3c0d655441f28b724ea6112625 *src/utilities.c
a90164d49e110942efc509a7592b4d7c *src/utilities.h
49343799ad87d4283c7e37b870209114 *src/vcffile.c
8a81687da9fb39f4995ba3df95d92964 *src/vcffile.h
c71e3141cfe80c5da172f9de2016d547 *src/vcftype.c
fa636a82e9d41d13bb4bb58bce901343 *src/vcftype.h
490666e59854522d642ed8baea51edd2 *src/writevcf.c
363b17e437fca22837b892ab3fcd1ef2 *src/writevcf.h
19ddb7954fc78f00c60fc5fff2eab422 *tests/VariantAnnotation_unit_tests.R
f0718d7188ef8d41ef2896978b203e5b *vignettes/VariantAnnotation.Rmd
1cad9a1953295837c7d6ee0ebf1e5a52 *vignettes/bioinformatics.csl
05c866a0b1b4cdc9885e0aa6506955a1 *vignettes/ens.bib
c0424a9efefad07f22be4677ee2c2037 *vignettes/ensemblVEP.Rmd
9437f0796f440360ce0daffdb87e7cb1 *vignettes/filterVcf.Rmd
091a35ba1c71e98e1dac87d5830ac7fa *vignettes/filterVcf.bib
|